The comments came during a town hall meeting Fantino organized in September shortly after becoming minister. The event cost $25,000, and featured a motivational speaker and a question-and-answer session with Fantino.
The event was billed by senior executives as a way for Fantino to have a "personal and wholesome interaction" with the agency's approximately 1,200 employees. CIDA had just lost $319.2 million in the government's deficit-reduction exercise.
Documents and a recording of the town hall were obtained by The Canadian Press under the Access to Information Act.
Early in the meeting, a 12-year employee raised the issue of the centralization of control inside the minister's office.
"Let's say very narrow access to the Minister's office and the fact that the advice that we work very hard to provide has met with some tendencies of self-censorship," the bureaucrat said, adding that decisions used to be made in the field.
"These are fundamental things that you have no clue how much it can impair our ability to actually deliver things when there's no agility of the system to be able to implement without always having to go back and forth (through) 17 versions of a memo..."
Fantino did not answer the question directly, but emphasized he had an "open door policy" towards employee.
"At the end of the day if things go sideways I have no one else to take a bow but me," he said. "I take that responsibility very seriously."
Another bureaucrat said the agency needed to give its staff more freedom to talk publicly about their activities. Prime Minister Stephen Harper instituted a highly centralized system of communications when he came to office in 2006, clamping down on the ability of bureaucrats and diplomats to speak to the media.
"I'm just back from three years overseas in a field mission and I found it was unfortunate that we were at the time not always empowered to be able to tell the right story, tell the story, tell what CIDA is doing," said the staffer.
Fantino said he agreed that it was important to spread the word about CIDA, but with caution.
"I think we need to empower our people within parameters. We won't want any independent agents going out there and sort of throwing us into ... things can happen very quickly as you well know," Fantino said.
Fantino was recently put on the defensive when two highly political statements attacking the opposition parties were posted to the department's website. Government websites and communications are supposed to be non-partisan.
Fantino's office said at the time that the statements were posted in error, and they were removed from the site.
At least one sensitive question that had been submitted by an employee before meeting did not wind up getting posed. It dealt with the Conservative government's new focus on partnering with the mining sector in the developing world to deliver assistance.
"You should be aware that the new natural resources framework in the agency, particularly mining, has created unease among the agency's employees," one staff member from the Haiti program wrote.
"The media made a big deal out of this, and it's a debate that's elicited a lot of discussions about people's values and our raison d'etre as an agency.
"Based on what you've seen on the ground last week (in Africa) how do you see this new framework fitting with CIDA's mandate?"
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